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Turabi K, Klute K, Radhakrishnan P. Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies. Cancers (Basel) 2024; 16:2432. [PMID: 39001494 PMCID: PMC11240538 DOI: 10.3390/cancers16132432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.
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Affiliation(s)
- Khadija Turabi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey Klute
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Cardelli M, Marchegiani F, Stripoli P, Piacenza F, Recchioni R, Di Rosa M, Giacconi R, Malavolta M, Galeazzi R, Arosio B, Cafarelli F, Spannella F, Cherubini A, Lattanzio F, Olivieri F. Plasma cfDNA abundance as a prognostic biomarker for higher risk of death in geriatric cardiovascular patients. Mech Ageing Dev 2024; 219:111934. [PMID: 38604436 DOI: 10.1016/j.mad.2024.111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
The management of geriatric cardiovascular disease (CVD) patients with multimorbidity remains challenging and could potentially be improved by integrating clinical data with innovative prognostic biomarkers. In this context, the analysis of circulating analytes, including cell-free DNA (cfDNA), appears particularly promising. Here, we investigated circulating cfDNA (measured through the quantification of 247 bp and 115 bp Alu genomic fragments) in a cohort of 244 geriatric CVD patients with multimorbidity hospitalised for acute CVD or non-CVD events. Survival analysis showed a direct association between Alu 247 cfDNA abundance and risk of death, particularly evident in the first six months after admission for acute CVD events. Higher plasma cfDNA concentration was associated with mortality in the same period of time. The cfDNA integrity (Alu 247/115), although not associated with outcome, appeared to be useful in discriminating patients in whom Alu 247 cfDNA abundance is most effective as a prognostic biomarker. The cfDNA parameters were associated with several biochemical markers of inflammation and myocardial damage. In conclusion, an increase in plasma cfDNA abundance at hospital admission is indicative of a higher risk of death in geriatric CVD patients, especially after acute CVD events, and its analysis may be potentially useful for risk stratification.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | | | - Pierpaolo Stripoli
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Rina Recchioni
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Mirko Di Rosa
- Centre for Biostatistics and Applied Geriatric Clinical Epidemiology, IRCCS INRCA, Ancona 60124, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Roberta Galeazzi
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Beatrice Arosio
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | | | - Francesco Spannella
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, Ancona 60127, Italy; Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60126, Italy
| | - Antonio Cherubini
- Geriatria, Accettazione Geriatrica e Centro di Ricerca per L'invecchiamento, IRCCS INRCA, Ancona 60127, Italy
| | | | - Fabiola Olivieri
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy; Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60126, Italy; Scientific Direction, IRCCS INRCA, Ancona, Italy
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Bleckman RF, Haag CMSC, Rifaela N, Beukema G, Mathijssen RHJ, Steeghs N, Gelderblom H, Desar IME, Cleven A, Ter Elst A, Schuuring E, Reyners AKL. Levels of circulating tumor DNA correlate with tumor volume in gastro-intestinal stromal tumors: an exploratory long-term follow-up study. Mol Oncol 2024. [PMID: 38790141 DOI: 10.1002/1878-0261.13644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 05/26/2024] Open
Abstract
Patients with gastro-intestinal stromal tumors (GISTs) undergoing tyrosine kinase inhibitor therapy are monitored with regular computed tomography (CT) scans, exposing patients to cumulative radiation. This exploratory study aimed to evaluate circulating tumor DNA (ctDNA) testing to monitor treatment response and compare changes in ctDNA levels with RECIST 1.1 and total tumor volume measurements. Between 2014 and 2021, six patients with KIT proto-oncogene, receptor tyrosine kinase (KIT) exon-11-mutated GIST from whom long-term plasma samples were collected prospectively were included in the study. ctDNA levels of relevant plasma samples were determined using the KIT exon 11 digital droplet PCR drop-off assay. Tumor volume measurements were performed using a semi-automated approach. In total, 94 of 130 clinically relevant ctDNA samples were analyzed. Upon successful treatment response, ctDNA became undetectable in all patients. At progressive disease, ctDNA was detectable in five out of six patients. Higher levels of ctDNA correlated with larger tumor volumes. Undetectable ctDNA at the time of progressive disease on imaging was consistent with lower tumor volumes compared to those with detectable ctDNA. In summary, ctDNA levels seem to correlate with total tumor volume at the time of progressive disease. Our exploratory study shows promise for including ctDNA testing in treatment follow-up.
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Affiliation(s)
- Roos F Bleckman
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Charlotte M S C Haag
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Naomi Rifaela
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Gerrieke Beukema
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute Antoni van Leeuwenhoek, Amsterdam, The Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Ingrid M E Desar
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen Cleven
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
- Department of Medical Oncology, Leiden University Medical Center, The Netherlands
| | - Arja Ter Elst
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Ed Schuuring
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Anna K L Reyners
- Department of Medical Oncology and Pathology, University Medical Center Groningen, University of Groningen, The Netherlands
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Dennhardt S, Ceanga IA, Baumbach P, Amiratashani M, Kröller S, Coldewey SM. Cell-free DNA in patients with sepsis: long term trajectory and association with 28-day mortality and sepsis-associated acute kidney injury. Front Immunol 2024; 15:1382003. [PMID: 38803503 PMCID: PMC11128621 DOI: 10.3389/fimmu.2024.1382003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/09/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Outcome-prediction in patients with sepsis is challenging and currently relies on the serial measurement of many parameters. Standard diagnostic tools, such as serum creatinine (SCr), lack sensitivity and specificity for acute kidney injury (AKI). Circulating cell-free DNA (cfDNA), which can be obtained from liquid biopsies, can potentially contribute to the quantification of tissue damage and the prediction of sepsis mortality and sepsis-associated AKI (SA-AKI). Methods We investigated the clinical significance of cfDNA levels as a predictor of 28-day mortality, the occurrence of SA-AKI and the initiation of renal replacement therapy (RRT) in patients with sepsis. Furthermore, we investigated the long-term course of cfDNA levels in sepsis survivors at 6 and 12 months after sepsis onset. Specifically, we measured mitochondrial DNA (mitochondrially encoded NADH-ubiquinone oxidoreductase chain 1, mt-ND1, and mitochondrially encoded cytochrome C oxidase subunit III, mt-CO3) and nuclear DNA (nuclear ribosomal protein S18, n-Rps18) in 81 healthy controls and all available samples of 150 intensive care unit patients with sepsis obtained at 3 ± 1 days, 7 ± 1 days, 6 ± 2 months and 12 ± 2 months after sepsis onset. Results Our analysis revealed that, at day 3, patients with sepsis had elevated levels of cfDNA (mt-ND1, and n-Rps18, all p<0.001) which decreased after the acute phase of sepsis. 28-day non-survivors of sepsis (16%) had higher levels of cfDNA (all p<0.05) compared with 28-day survivors (84%). Patients with SA-AKI had higher levels of cfDNA compared to patients without AKI (all p<0.05). Cell-free DNA was also significantly increased in patients requiring RRT (all p<0.05). All parameters improved the AUC for SCr in predicting RRT (AUC=0.88) as well as APACHE II in predicting mortality (AUC=0.86). Conclusion In summary, cfDNA could potentially improve risk prediction models for mortality, SA-AKI and RRT in patients with sepsis. The predictive value of cfDNA, even with a single measurement at the onset of sepsis, could offer a significant advantage over conventional diagnostic methods that require repeated measurements or a baseline value for risk assessment. Considering that our data show that cfDNA levels decrease after the first insult, future studies could investigate cfDNA as a "memoryless" marker and thus bring further innovation to the complex field of SA-AKI diagnostics.
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Affiliation(s)
- Sophie Dennhardt
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Iuliana-Andreea Ceanga
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Philipp Baumbach
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Mona Amiratashani
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Sarah Kröller
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Sina M. Coldewey
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Septomics Research Centre, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
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Morisi N, Virzì GM, Ferrarini M, Alfano G, Zanella M, Ronco C, Donati G. Exploring the Role of Cell-Free Nucleic Acids and Peritoneal Dialysis: A Narrative Review. Genes (Basel) 2024; 15:553. [PMID: 38790182 PMCID: PMC11121405 DOI: 10.3390/genes15050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Cell-free nucleic acids (cf-NAs) represent a promising biomarker of various pathological and physiological conditions. Since its discovery in 1948, cf-NAs gained prognostic value in oncology, immunology, and other relevant fields. In peritoneal dialysis (PD), blood purification is performed by exposing the peritoneal membrane. Relevant sections: Complications of PD such as acute peritonitis and peritoneal membrane aging are often critical in PD patient management. In this review, we focused on bacterial DNA, cell-free DNA, mitochondrial DNA (mtDNA), microRNA (miRNA), and their potential uses as biomarkers for monitoring PD and its complications. For instance, the isolation of bacterial DNA in early acute peritonitis allows bacterial identification and subsequent therapy implementation. Cell-free DNA in peritoneal dialysis effluent (PDE) represents a marker of stress of the peritoneal membrane in both acute and chronic PD complications. Moreover, miRNA are promising hallmarks of peritoneal membrane remodeling and aging, even before its manifestation. In this scenario, with multiple cytokines involved, mtDNA could be considered equally meaningful to determine tissue inflammation. CONCLUSIONS This review explores the relevance of cf-NAs in PD, demonstrating its promising role for both diagnosis and treatment. Further studies are necessary to implement the use of cf-NAs in PD clinical practice.
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Affiliation(s)
- Niccolò Morisi
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Grazia Maria Virzì
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Marco Ferrarini
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Gaetano Alfano
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
| | - Monica Zanella
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Claudio Ronco
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Gabriele Donati
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
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de Miranda FS, Claudio LMAM, de Almeida DSM, Nunes JB, Barauna VG, Luiz WB, Vassallo PF, Campos LCG. Cell-Free Nuclear and Mitochondrial DNA as Potential Biomarkers for Assessing Sepsis Severity. Biomedicines 2024; 12:933. [PMID: 38790895 PMCID: PMC11117867 DOI: 10.3390/biomedicines12050933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Sepsis continues to be a significant public health challenge despite advances in understanding its pathophysiology and management strategies. Therefore, this study evaluated the value of cell-free nuclear DNA (cf-nDNA) and cell-free mitochondrial DNA (cf-mtDNA) for assessing the severity and prognosis of sepsis. Ninety-four patients were divided into three groups: infection (n = 32), sepsis (n = 30), and septic shock (n = 32). Plasma samples were collected at the time of diagnosis, and cfDNA concentrations were determined by qPCR assay. The results showed that plasma cfDNA levels increased with the severity of the disease. To distinguish between patients with infection and those with sepsis, the biomarker L1PA290 achieved the highest AUC of 0.817 (95% CI: 0.725-0.909), demonstrating a sensitivity of 77.0% and a specificity of 79.3%. When cf-nDNA was combined with the SOFA score, there was a significant improvement in the AUC (0.916 (0.853-0.979)), sensitivity (88.1%), and specificity (80.0%). Moreover, patients admitted to the ICU after being diagnosed with sepsis had significantly higher cf-nDNA concentrations. In patients admitted to the ICU, combining cf-nDNA with the SOFA score yielded an AUC of 0.753 (0.622-0.857), with a sensitivity of 95.2% and a specificity of 50.0%. cfDNA can differentiate between patients with infection and those with sepsis. It can also identify patients who are likely to be admitted to the ICU by predicting those with indications for intensive care, suggesting its potential as a biomarker for sepsis.
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Affiliation(s)
- Felipe Silva de Miranda
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Livia Maria A. M. Claudio
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil;
| | - Dayanne Silva M. de Almeida
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Juliana Braga Nunes
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil;
| | - Wilson Barros Luiz
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Paula Frizzera Vassallo
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil;
| | - Luciene Cristina Gastalho Campos
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
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Datta P, Rattan D, Sharma D, Sharma N, Kalra N, Duseja A, Angrup A, Sehgal R. Novel diagnostic approach for amoebic liver abscess using cell free (cf) DNA: a prospective study. Infect Dis (Lond) 2024; 56:259-267. [PMID: 38112684 DOI: 10.1080/23744235.2023.2294119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Amoebic liver abscess (ALA) is commonly seen in tropical countries and diagnosis of ALA relies mainly on non-specific serological and imaging techniques as well as PCR from pus. OBJECTIVE This study evaluated the potential of using cell free DNA (cfDNA) from serum and urine for diagnosing ALA. METHODS We prospectively evaluated quantitative PCR (qPCR) for detection of cf DNA in serum and urine sample in all liver abscess patients. The samples were collected from patients reporting to emergency ward of Postgraduate Institute of Medical Education and Research, Chandigarh, India with symptoms suggestive of liver abscess. Real time PCR was done to detect cf DNA in serum and urine by targeting 99-bp unit of small subunit rRNA of Entamoeba histolytica and conventional PCR for pus. RESULTS A total 113 samples (serum and urine) and 100 pus samples were analysed. A total of 62 ALA patients were confirmed; with maximum 57 patients detected by qPCR for cfDNA in the serum, 55 patients by PCR on pus aspirate and 50 ALA patients by qPCR for cfDNA in urine sample. Therefore, the sensitivity of qPCR for detection of cf DNA in serum was 91.94% and for urine was 80.65%. CONCLUSION A total of 11.2% of ALA patients were diagnosed only through detection of E. histolytica cf DNA in their serum and urine. Detection of cfDNA from serum, urine of ALA has a potential role in future especially for developing countries as it is a rapid, sensitive and patient friendly diagnostic approach.
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Affiliation(s)
- Priya Datta
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Divya Rattan
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Devyani Sharma
- Department of Medical Parasitology, PGIMER, Chandigarh, India
| | - Navneet Sharma
- Department of Internal Medicine, PGIMER, Chandigarh, India
| | - Naveen Kalra
- Department of Radiodiagnosis & Imaging, PGIMER, Chandigarh, India
| | - Ajay Duseja
- Department of Hepatology, PGIMER, Chandigarh, India
| | - Archana Angrup
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, PGIMER, Chandigarh, India
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Díaz del Arco C, Fernández Aceñero MJ, Ortega Medina L. Liquid biopsy for gastric cancer: Techniques, applications, and future directions. World J Gastroenterol 2024; 30:1680-1705. [PMID: 38617733 PMCID: PMC11008373 DOI: 10.3748/wjg.v30.i12.1680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
After the study of circulating tumor cells in blood through liquid biopsy (LB), this technique has evolved to encompass the analysis of multiple materials originating from the tumor, such as nucleic acids, extracellular vesicles, tumor-educated platelets, and other metabolites. Additionally, research has extended to include the examination of samples other than blood or plasma, such as saliva, gastric juice, urine, or stool. LB techniques are diverse, intricate, and variable. They must be highly sensitive, and pre-analytical, patient, and tumor-related factors significantly influence the detection threshold, diagnostic method selection, and potential results. Consequently, the implementation of LB in clinical practice still faces several challenges. The potential applications of LB range from early cancer detection to guiding targeted therapy or immunotherapy in both early and advanced cancer cases, monitoring treatment response, early identification of relapses, or assessing patient risk. On the other hand, gastric cancer (GC) is a disease often diagnosed at advanced stages. Despite recent advances in molecular understanding, the currently available treatment options have not substantially improved the prognosis for many of these patients. The application of LB in GC could be highly valuable as a non-invasive method for early diagnosis and for enhancing the management and outcomes of these patients. In this comprehensive review, from a pathologist's perspective, we provide an overview of the main options available in LB, delve into the fundamental principles of the most studied techniques, explore the potential utility of LB application in the context of GC, and address the obstacles that need to be overcome in the future to make this innovative technique a game-changer in cancer diagnosis and treatment within clinical practice.
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Affiliation(s)
- Cristina Díaz del Arco
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - M Jesús Fernández Aceñero
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Luis Ortega Medina
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
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9
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Varzaru B, Iacob RA, Bunduc S, Manea I, Sorop A, Spiridon A, Chelaru R, Croitoru A, Topala M, Becheanu G, Dumbrava M, Dima S, Popescu I, Gheorghe C. Prognostic Value of Circulating Cell-Free DNA Concentration and Neutrophil-to-Lymphocyte Ratio in Patients with Pancreatic Ductal Adenocarcinoma: A Prospective Cohort Study. Int J Mol Sci 2024; 25:2854. [PMID: 38474101 DOI: 10.3390/ijms25052854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (ccfDNA) quantity correlates with the clinical characteristics and prognosis of various cancer types. We investigated whether ccfDNA levels and the neutrophil-to-lymphocyte ratio (NLR) have prognostic value in patients with pancreatic ductal adenocarcinoma (PDAC). Peripheral blood was collected from 82 patients with PDAC prior to any diagnostic procedure or the administration of chemotherapy. Plasma DNA was isolated, and ccfDNA concentration and NLR were determined. We found that ccfDNA levels were correlated with age and tumor burden. Moreover, higher values of NLR (≥3.31) were linked with worse overall survival (OS) (4 vs. 10 months; log rank p = 0.011), and an elevated ccfDNA concentration (≥25.79 ng/mL) was strongly associated with shorter OS (4 vs. 8 months; log rank p = 0.009). According to the results of the multivariable Cox regression analysis, the baseline concentration of ccfDNA was an independent prognostic factor for OS (HR 0.45, 95% CI 0.21-0.97, p = 0.041). Furthermore, the combination of ccfDNA levels with NLR greatly enhanced the prognostic accuracy of PDAC patients. Our study demonstrates that ccfDNA concentration and NLR are independent predictors of survival in PDAC. Subsequent studies should validate this combination as a prognostic indicator in PDAC patients and assess its utility for guiding therapeutic decisions.
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Affiliation(s)
- Bianca Varzaru
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Razvan Andrei Iacob
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Stefania Bunduc
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Ioana Manea
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andrei Sorop
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Andreea Spiridon
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Raluca Chelaru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Adina Croitoru
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Mihaela Topala
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
| | - Gabriel Becheanu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Mona Dumbrava
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Simona Dima
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Irinel Popescu
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
| | - Cristian Gheorghe
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Center of Excellence in Translational Medicine, Fundeni Clinical Institute, 022328 Bucharest, Romania
- Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, 022238 Bucharest, Romania
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10
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De La Cruz-Sigüenza DA, Reyes-Grajeda JP, Velasco-Velázquez MA, Trejo-Becerril C, Pérez-Cárdenas E, Chávez-Blanco A, Taja-Chayeb L, Domínguez-Gómez G, Ramos-Godinez MP, González-Fierro A, Dueñas-González A. The non-vesicle cell-free DNA (cfDNA) induces cell transformation associated with horizontal DNA transfer. Mol Biol Rep 2024; 51:174. [PMID: 38252353 PMCID: PMC10803523 DOI: 10.1007/s11033-023-09016-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Cell-free DNA (cfDNA) is a source for liquid biopsy used for cancer diagnosis, therapy selection, and disease monitoring due to its non-invasive nature and ease of extraction. However, cfDNA also participates in cancer development and progression by horizontal transfer. In humans, cfDNA circulates complexed with extracellular vesicles (EV) and macromolecular complexes such as nucleosomes, lipids, and serum proteins. The present study aimed to demonstrate whether cfDNA not associated with EV induces cell transformation and tumorigenesis. METHODS Supernatant of the SW480 human colon cancer cell line was processed by ultracentrifugation to obtain a soluble fraction (SF) and a fraction associated with EV (EVF). Primary murine embryonic fibroblast cells (NIH3T3) underwent passive transfection with these fractions, and cell proliferation, cell cycle, apoptosis, cell transformation, and tumorigenic assays were performed. Next, cfDNA was analyzed by electronic microscopy, and horizontal transfer was assessed by human mutant KRAS in recipient cells via PCR and recipient cell internalization via fluorescence microscopy. RESULTS The results showed that the SF but not the EVF of cfDNA induced proliferative and antiapoptotic effects, cell transformation, and tumorigenesis in nude mice, which were reduced by digestion with DNAse I and proteinase K. These effects were associated with horizontal DNA transfer and cfDNA internalization into recipient cells. CONCLUSIONS The results suggest pro-tumorigenic effects of cfDNA in the SF that can be offset by enzyme treatment. Further exploration of the horizontal tumor progression phenomenon mediated by cfDNA is needed to determine whether its manipulation may play a role in cancer therapy.
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Affiliation(s)
- D A De La Cruz-Sigüenza
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - J P Reyes-Grajeda
- Protein Structure Laboratory, Instituto Nacional de Medicina Genomica (INMEGEN), Tlalpan, 14610, Mexico City, Mexico
| | - M A Velasco-Velázquez
- Department of Pharmacology, Faculty of Medicine, Universidad Nacional Autónoma de México (UNAM), Coyoacan, 04510, Mexico City, Mexico
| | - C Trejo-Becerril
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - E Pérez-Cárdenas
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A Chávez-Blanco
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - L Taja-Chayeb
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - G Domínguez-Gómez
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - M P Ramos-Godinez
- Department of Pathology, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A González-Fierro
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico
| | - A Dueñas-González
- Subdirection of Basic Research, Instituto Nacional de Cancerología (INCan), Tlalpan, 14080, Mexico City, Mexico.
- Department of Genomic Medicine and Environmental Toxicology, Institute of Biomedical Research, Universidad Nacional Autonoma de Mexico (UNAM), Av. Universidad 3004, Copilco Universidad, Coyoacan, 04510, Mexico City, Mexico.
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11
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Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024; 31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.
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Affiliation(s)
- Yajuan Gao
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Nanyang Zhou
- Department of Traditional Chinese Medicine, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jie Liu
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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12
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Chimbangu CT, Ya Z, Xi L, Jiayue Z, Xiao M, Ying W, Xingxu Y, Liu X. Promising response of dabrafenib, trametinib, and osimertinib combination therapy for concomitant BRAF and EGFR-TKI resistance mutations. Anticancer Drugs 2024; 35:109-115. [PMID: 37578745 PMCID: PMC10720804 DOI: 10.1097/cad.0000000000001537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/20/2023] [Indexed: 08/15/2023]
Abstract
Despite the initial promise of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) in effectively combating tumor growth, the majority of patients with advanced non-small cell lung cancers (NSCLCs) inevitably develop resistance to these treatments. An infrequent genetic mutation known as BRAFV600E has been identified as a contributing factor to the emergence of acquired resistance to EGFR-TKIs. Genetic alterations in BRAF, particularly V600E, contribute to resistance to osimertinib. However, a combination therapy involving osimertinib, dabrafenib (a BRAF inhibitor), and trametinib has shown effectiveness in overcoming BRAF V600E-mediated resistance in advanced lung adenocarcinoma. This treatment regimen holds promise for similar cases. In our case report, the combination of osimertinib, dabrafenib, and trametinib effectively overcame osimertinib resistance and resulted in sustained partial remission.
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Affiliation(s)
- Clint Taonaishe Chimbangu
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Zhou Ya
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Li Xi
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Zhao Jiayue
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Meng Xiao
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Wang Ying
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Yu Xingxu
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
| | - Xiaomei Liu
- Department of Oncology, the First Affiliated Hospital of Jinzhou Medical University, Liaoning, Jinzhou, China
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13
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Charoensappakit A, Sae-Khow K, Rattanaliam P, Vutthikraivit N, Pecheenbuvan M, Udomkarnjananun S, Leelahavanichkul A. Cell-free DNA as diagnostic and prognostic biomarkers for adult sepsis: a systematic review and meta-analysis. Sci Rep 2023; 13:19624. [PMID: 37949942 PMCID: PMC10638380 DOI: 10.1038/s41598-023-46663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Although cell-free DNA (cfDNA) is an emerging sepsis biomarker, the use of cfDNA, especially as diagnostic and prognostic indicators, has surprisingly not been systemically analyzed. Data of adult patients with sepsis that conducted cfDNA measurement within 24 h of the admission was collected from PubMed, ScienceDirect, Scopus, and Cochrane Library until October 2022. The Quality in Prognosis Studies (QUIPS) and Quality Assessment in Diagnostic Studies-2 (QUADAS-2) tools were used to reduce the risk of biased assessment. The mean difference (MD) of cfDNA concentration and the standardized mean difference (SMD) between populations was calculated using Review Manager (RevMan) version 5.4.1 package software. Pooled analysis from 18 included studies demonstrated increased serum cfDNA levels in sepsis when compared with healthy control (SMD = 1.02; 95% confidence interval (CI) 0.46-1.57) or non-sepsis patients in the intensive care unit (ICU) (SMD = 1.03; 95% CI 0.65-1.40), respectively. Meanwhile, a slight decrease in the statistical value was observed when compared with non-sepsis ICU patients with SIRS (SMD = 0.74; 95% 0.41-1.06). The lower cfDNA levels were also observed in sepsis survivors compared to the non-survivors (SMD at 1.43; 95%CI 0.69-2.17) with the pooled area under the receiver operating characteristic curve (AUC) of 0.76 (95% CI 0.64-0.87) for the mortality prediction. Levels of cfDNA showed a pooled sensitivity of 0.81 (95% CI 0.75-0.86) and specificity of 0.72 (95% CI 0.65-0.78) with pooled diagnostic odd ratio (DOR) at 25.03 (95% CI 5.48-114.43) for the identification of sepsis in critically ill conditions. The cfDNA levels were significantly higher in patients with sepsis and being a helpful indicator for the critically ill conditions of sepsis. Nevertheless, results of the test must be interpreted carefully with the context of all clinical situations.
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Affiliation(s)
- Awirut Charoensappakit
- Medical Microbiology, Interdisciplinary and International Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicines, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kritsanawan Sae-Khow
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicines, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pongpera Rattanaliam
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nuntanuj Vutthikraivit
- Division of Critical Care Medicine, Department of Internal Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Monvasi Pecheenbuvan
- Division of Critical Care Medicine, Department of Internal Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Suwasin Udomkarnjananun
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence on Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicines, Chulalongkorn University, Bangkok, 10330, Thailand.
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Yang Y, Gao Y, Zhang M, Qian H, Zhao K, Wang W, Ma Y, Zhang D, Li X, Hu F, Sun X. Genetic diagnosis of a rare COL7A1 variant causing dystrophic epidermolysis bullosa pruriginosa through whole‑exome sequencing. Exp Ther Med 2023; 26:502. [PMID: 37822584 PMCID: PMC10562958 DOI: 10.3892/etm.2023.12201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/25/2023] [Indexed: 10/13/2023] Open
Abstract
Dystrophic epidermolysis bullosa pruriginosa (DEB-Pr) is a rare subtype of inherited DEB. In the present study, whole-exome sequencing was conducted on 12 individuals from the same affected family and a rare heterozygous variation was identified in the collagen type VII, α1 (COL7A1) gene, namely c.6859G>A (p.Gly2287Arg). Subsequently, this heterozygous variant was confirmed using Sanger sequencing of individual plasma cell-free DNA (cfDNA) and it was demonstrated for the first time, to the best of our knowledge, that COL7A1 exons can be amplified from plasma cfDNA. Within the large pedigree examined, 14 out of 18 individuals carried the variant, 3 carried the wild type, and one exceptional case, III-9, showed no disease symptoms despite carrying the disease variant. A general association between genotype and phenotype was established. Of note, the mutation landscape indicated that this G2287R variant is primarily reported in Asian countries. In silico structure prediction suggested that the residue resulting from the mutation may affect collagen protein stability. In conclusion, the present study provides evidence for the involvement of the COL7A1 G2287R gene variant in the development of DEB-Pr and highlights the potential utility of cfDNA in genetic disease diagnosis.
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Affiliation(s)
- Yanhui Yang
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Yangmin Gao
- Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province, The Affiliated Dermatology Hospital of Nanchang University, Nanchang, Jiangxi 330200, P.R. China
| | - Mengna Zhang
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Hua Qian
- Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province, The Affiliated Dermatology Hospital of Nanchang University, Nanchang, Jiangxi 330200, P.R. China
- Department of Laboratory Medicine, Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Ke Zhao
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Weijuan Wang
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Yanxiu Ma
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Dan Zhang
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
| | - Xiaoguang Li
- Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province, The Affiliated Dermatology Hospital of Nanchang University, Nanchang, Jiangxi 330200, P.R. China
- Department of Laboratory Medicine, Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, P.R. China
| | - Fengming Hu
- Jiangxi Provincial Clinical Research Center for Skin Diseases, Dermatology Hospital of Jiangxi Province, The Affiliated Dermatology Hospital of Nanchang University, Nanchang, Jiangxi 330200, P.R. China
| | - Xiaoming Sun
- Key Laboratory of Aging and Cancer Biology, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P.R. China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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15
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Bahado‐Singh RO, Turkoglu O, Aydas B, Vishweswaraiah S. Precision oncology: Artificial intelligence, circulating cell-free DNA, and the minimally invasive detection of pancreatic cancer-A pilot study. Cancer Med 2023; 12:19644-19655. [PMID: 37787018 PMCID: PMC10587955 DOI: 10.1002/cam4.6604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is among the most lethal cancers. The lack of effective tools for early detection results in late tumor detection and, consequently, high mortality rate. Precision oncology aims to develop targeted individual treatments based on advanced computational approaches of omics data. Biomarkers, such as global alteration of cytosine (CpG) methylation, can be pivotal for these objectives. In this study, we performed DNA methylation profiling of pancreatic cancer patients using circulating cell-free DNA (cfDNA) and artificial intelligence (AI) including Deep Learning (DL) for minimally invasive detection to elucidate the epigenetic pathogenesis of PC. METHODS The Illumina Infinium HD Assay was used for genome-wide DNA methylation profiling of cfDNA in treatment-naïve patients. Six AI algorithms were used to determine PC detection accuracy based on cytosine (CpG) methylation markers. Additional strategies for minimizing overfitting were employed. The molecular pathogenesis was interrogated using enrichment analysis. RESULTS In total, we identified 4556 significantly differentially methylated CpGs (q-value < 0.05; Bonferroni correction) in PC versus controls. Highly accurate PC detection was achieved with all 6 AI platforms (Area under the receiver operator characteristics curve [0.90-1.00]). For example, DL achieved AUC (95% CI): 1.00 (0.95-1.00), with a sensitivity and specificity of 100%. A separate modeling approach based on logistic regression-based yielded an AUC (95% CI) 1.0 (1.0-1.0) with a sensitivity and specificity of 100% for PC detection. The top four biological pathways that were epigenetically altered in PC and are known to be linked with cancer are discussed. CONCLUSION Using a minimally invasive approach, AI, and epigenetic analysis of circulating cfDNA, high predictive accuracy for PC was achieved. From a clinical perspective, our findings suggest that that early detection leading to improved overall survival may be achievable in the future.
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Affiliation(s)
- Ray O. Bahado‐Singh
- Department of Obstetrics and GynecologyCorewell Health – William Beaumont University HospitalRoyal OakMichiganUSA
| | - Onur Turkoglu
- Department of Obstetrics and GynecologyCorewell Health – William Beaumont University HospitalRoyal OakMichiganUSA
| | - Buket Aydas
- Department of Care Management AnalyticsBlue Cross Blue Shield of MichiganDetroitMichiganUSA
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Hoeter K, Neuberger E, Fischer S, Herbst M, Juškevičiūtė E, Enders K, Rossmann H, Sprinzl MF, Simon P, Bodenstein M, Schaefer M. Evidence for the utility of cfDNA plasma concentrations to predict disease severity in COVID-19: a retrospective pilot study. PeerJ 2023; 11:e16072. [PMID: 37744227 PMCID: PMC10512938 DOI: 10.7717/peerj.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/20/2023] [Indexed: 09/26/2023] Open
Abstract
Background COVID-19 is a worldwide pandemic caused by the highly infective SARS-CoV-2. There is a need for biomarkers not only for overall prognosis but also for predicting the response to treatments and thus for improvements in the clinical management of patients with COVID-19. Circulating cell-free DNA (cfDNA) has emerged as a promising biomarker in the assessment of various pathological conditions. The aim of this retrospective and observational pilot study was to investigate the range of cfDNA plasma concentrations in hospitalized COVID-19 patients during the first wave of SARS-CoV-2 infection, to relate them to established inflammatory parameters as a correlative biomarker for disease severity, and to compare them with plasma levels in a healthy control group. Methods Lithium-Heparin plasma samples were obtained from COVID-19 patients (n = 21) during hospitalization in the University Medical Centre of Mainz, Germany between March and June 2020, and the cfDNA concentrations were determined by quantitative PCR yielding amplicons of long interspersed nuclear elements (LINE-1). The cfDNA levels were compared with those of an uninfected control group (n = 19). Results Plasma cfDNA levels in COVID-19 patients ranged from 247.5 to 6,346.25 ng/ml and the mean concentration was 1,831 ± 1,388 ng/ml (± standard deviation), which was significantly different from the levels of the uninfected control group (p < 0.001). Regarding clinical complications, the highest correlation was found between cfDNA levels and the myositis (p = 0.049). In addition, cfDNA levels correlated with the "WHO clinical progression scale". D-Dimer and C-reactive protein (CRP) were the clinical laboratory parameters with the highest correlations with cfDNA levels. Conclusion The results of this observational pilot study show a wide range in cfDNA plasma concentrations in patients with COVID-19 during the first wave of infection and confirm that cfDNA plasma concentrations serve as a predictive biomarker of disease severity in COVID-19.
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Affiliation(s)
- Katharina Hoeter
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Elmo Neuberger
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Susanne Fischer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Manuel Herbst
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Ema Juškevičiūtė
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Kira Enders
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Martin F. Sprinzl
- Department of Internal Medicine I, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Disease Prevention and Rehabilitation, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Marc Bodenstein
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
| | - Michael Schaefer
- Department of Anaesthesiology, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
- Focus Program Translational Neurosciences (FTN), Johannes Gutenberg-University, Mainz, Germany
- Research Center for Immunotherapy, University Medical Centre of the Johannes Gutenberg-University, Mainz, Germany
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. The Diagnostic, Prognostic, and Therapeutic Potential of Cell-Free DNA with a Special Focus on COVID-19 and Other Viral Infections. Int J Mol Sci 2023; 24:14163. [PMID: 37762464 PMCID: PMC10532175 DOI: 10.3390/ijms241814163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-free DNA (cfDNA) in human blood serum, urine, and other body fluids recently became a commonly used diagnostic marker associated with various pathologies. This is because cfDNA enables a much higher sensitivity than standard biochemical parameters. The presence of and/or increased level of cfDNA has been reported for various diseases, including viral infections, including COVID-19. Here, we review cfDNA in general, how it has been identified, where it can derive from, its molecular features, and mechanisms of release and clearance. General suitability of cfDNA for diagnostic questions, possible shortcomings and future directions are discussed, with a special focus on coronavirus infection.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, Yerevan 0025, Armenia; (G.H.); (T.H.); (R.A.)
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
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Sikora JP, Karawani J, Sobczak J. Neutrophils and the Systemic Inflammatory Response Syndrome (SIRS). Int J Mol Sci 2023; 24:13469. [PMID: 37686271 PMCID: PMC10488036 DOI: 10.3390/ijms241713469] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
We are not entirely able to understand, assess, and modulate the functioning of the immune system in clinical situations that lead to a systemic inflammatory response. In the search for diagnostic and treatment strategies (which are still far from perfect), it became very important to study the pathogenesis and participation of endogenous inflammation mediators. This study attempts to more precisely establish the role of neutrophils in individual phenomena occurring during an inflammatory and anti-inflammatory reaction, taking into account their cidal, immunoregulatory, and reparative abilities. Pro- and anticoagulatory properties of endothelium in systemic inflammatory response syndrome (SIRS) are emphasised, along with the resulting clinical implications (the application of immunotherapy using mesenchymal stem/stromal cells (MSCs) or IL-6 antagonists in sepsis and COVID-19 treatment, among others). Special attention is paid to reactive oxygen species (ROS), produced by neutrophils activated during "respiratory burst" in the course of SIRS; the protective and pathogenic role of these endogenous mediators is highlighted. Moreover, clinically useful biomarkers of SIRS (neutrophil extracellular traps, cell-free DNA, DAMP, TREMs, NGAL, miRNA, selected cytokines, ROS, and recognised markers of endothelial damage from the group of adhesins by means of immunohistochemical techniques) related to the neutrophils are presented, and their role in the diagnosing and forecasting of sepsis, burn disease, and COVID-19 is emphasised. Finally, examples of immunomodulation of sepsis and antioxidative thermal injury therapy are presented.
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Affiliation(s)
- Janusz P. Sikora
- Department of Paediatric Emergency Medicine, 2nd Chair of Paediatrics, Central Clinical Hospital, Medical University of Łódź, ul. Sporna 36/50, 91-738 Łódź, Poland;
| | - Jakub Karawani
- Faculty of Medicine, Lazarski University, ul. Świeradowska 43, 02-662 Warsaw, Poland;
| | - Jarosław Sobczak
- Department of Paediatric Emergency Medicine, 2nd Chair of Paediatrics, Central Clinical Hospital, Medical University of Łódź, ul. Sporna 36/50, 91-738 Łódź, Poland;
- Department of Management and Logistics in Healthcare, Medical University of Łódź, ul. Lindleya 6, 90-131 Łódź, Poland
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19
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Noor J, Chaudhry A, Noor R, Batool S. Advancements and Applications of Liquid Biopsies in Oncology: A Narrative Review. Cureus 2023; 15:e42731. [PMID: 37654932 PMCID: PMC10466971 DOI: 10.7759/cureus.42731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
According to the World Health Organization (WHO), nearly 10 million people died from cancer worldwide in 2020, making it the leading cause of mortality. Liquid biopsies, which provide non-invasive and real-time monitoring of tumor dynamics, have evolved into innovative diagnostic techniques in the field of oncology. Liquid biopsies offer important insights into tumor heterogeneity, treatment response, minimum residual disease identification, and personalized treatment of cancer through the analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), extracellular vesicles, and microRNAs. They offer several advantages over traditional tissue biopsies, such as being less invasive, more convenient, more representative of tumor heterogeneity and dynamics, and more informative for guiding personalized treatment decisions. Liquid biopsies are being utilized increasingly in clinical oncology, particularly for patients with metastatic disease who require ongoing monitoring and treatment modification. In this narrative review article, we review the latest developments of liquid biopsy technologies, their applications and limitations, and their potential to transform diagnosis, prognosis, and management of cancer patients.
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Affiliation(s)
- Jawad Noor
- Internal Medicine, St. Dominic Hospital, Jackson, USA
| | | | - Riwad Noor
- Medicine/Public Health, Nishtar Hospital, Multan, PAK
| | - Saima Batool
- Pathology, Nishtar Medical University, Multan, PAK
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20
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Onofrei VA, Adam CA, Marcu DTM, Crisan Dabija R, Ceasovschih A, Constantin M, Grigorescu ED, Petroaie AD, Mitu F. Infective Endocarditis during Pregnancy-Keep It Safe and Simple! MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59050939. [PMID: 37241171 DOI: 10.3390/medicina59050939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
The diagnosis of infective endocarditis (IE) during pregnancy is accompanied by a poor prognosis for both mother and fetus in the absence of prompt management by multidisciplinary teams. We searched the electronic databases of PubMed, MEDLINE and EMBASE for clinical studies addressing the management of infective endocarditis during pregnancy, with the aim of realizing a literature review ranging from risk factors to diagnostic investigations to optimal therapeutic management for mother and fetus alike. The presence of previous cardiovascular pathologies such as rheumatic heart disease, congenital heart disease, prosthetic valves, hemodialysis, intravenous catheters or immunosuppression are the main risk factors predisposing patients to IE during pregnancy. The identification of modern risk factors such as intracardiac devices and intravenous drug administration as well as genetic diagnostic methods such as cell-free deoxyribonucleic acid (DNA) next-generation sequencing require that these cases be addressed in multidisciplinary teams. Guiding treatment to eradicate infection and protect the fetus simultaneously creates challenges for cardiologists and gynecologists alike.
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Affiliation(s)
- Viviana Aursulesei Onofrei
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Cristina Andreea Adam
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Cardiovascular Rehabilitation Clinic, Clinical Rehabilitation Hospital, Pantelimon Halipa Street No. 14, 700661 Iasi, Romania
| | - Dragos Traian Marius Marcu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Pneumophthisiology Iași, Doctor Iosif Cihac Street No. 30, 700115 Iasi, Romania
| | - Radu Crisan Dabija
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Clinical Hospital of Pneumophthisiology Iași, Doctor Iosif Cihac Street No. 30, 700115 Iasi, Romania
| | - Alexandr Ceasovschih
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Mihai Constantin
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- "St. Spiridon" Clinical Emergency Hospital, Independence Boulevard No. 1, 700111 Iasi, Romania
| | - Elena-Daniela Grigorescu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | - Antoneta Dacia Petroaie
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
| | - Florin Mitu
- Department of Medical Specialties I, II, III and Preventive Medicine and Interdisciplinary, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No. 16, 700115 Iasi, Romania
- Cardiovascular Rehabilitation Clinic, Clinical Rehabilitation Hospital, Pantelimon Halipa Street No. 14, 700661 Iasi, Romania
- Academy of Medical Sciences, Ion C. Brătianu Boulevard No. 1, 030167 Bucharest, Romania
- Academy of Romanian Scientists, Professor Dr. Doc. Dimitrie Mangeron Boulevard No. 433, 700050 Iasi, Romania
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21
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Nwafor JN, Torere BE, Agu E, Kadiku L, Ogunyemi T, Akinsanya PA, Araromi OO, Akahara DE, Okobi OE. The Role of Biomarkers in the Diagnosis and Prognosis of Different Stages of Melanoma. Cureus 2023; 15:e38693. [PMID: 37292567 PMCID: PMC10245076 DOI: 10.7759/cureus.38693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Melanoma is a skin cancer arising from melanocytes, the cells responsible for synthesizing melanin pigment, which gives the skin its color. Early diagnosis and treatment of melanoma increase survival rates. Clinical examination and biopsy are the primary tools used to diagnose melanoma. However, distinguishing between pre-malignant melanocytic lesions and early invasive melanoma histopathologically remains challenging. Therefore, additional modalities such as a detailed clinical history, imaging, genetic testing, and biomarkers have been applied to diagnose melanoma. This review discusses the current trends in biomarker advancements over the last 10 years to assist in the early detection and diagnosis of melanoma. Biomarkers such as melanoma-associated antigens (MAAs), S100B, microRNAs (miRNAs), and circulating tumor cells (CTCs) have the potential to aid in the detection, diagnosis, and prognosis of melanoma. However, the application of biomarkers in the diagnosis of melanoma is still evolving.
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Affiliation(s)
- Jane N Nwafor
- Internal Medicine, The University of District of Columbia, Silverspring, USA
| | | | - Evelyn Agu
- Biology, University of Texas, Arlington, USA
| | - Lateef Kadiku
- General Medicine, University of Lagos, Langhorne, USA
| | | | | | - Omoniyi O Araromi
- Pathology and Laboratory Medicine, University of Ibadan, University College Hospital, Ibadan, NGA
| | | | - Okelue E Okobi
- Family Medicine, Medficient Health Systems, Laurel, USA
- Family Medicine, Lakeside Medical Center, Belle Glade, USA
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22
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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23
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Cell-Free DNA in Plasma and Serum Indicates Disease Severity and Prognosis in Blunt Trauma Patients. Diagnostics (Basel) 2023; 13:diagnostics13061150. [PMID: 36980458 PMCID: PMC10047705 DOI: 10.3390/diagnostics13061150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
Background: Trauma is still a major cause of mortality in people < 50 years of age. Biomarkers are needed to estimate the severity of the condition and the patient outcome. Methods: Cell-free DNA (cfDNA) and further laboratory markers were determined in plasma and serum of 164 patients at time of admission to the emergency room. Among them were 64 patients with severe trauma (Injury Severity Score (ISS) ≥ 16), 51 patients with moderate trauma (ISS < 16) and 49 patients with single fractures (24 femur neck and 25 ankle fractures). Disease severity was objectified by ISS and Glasgow Coma Scale (GCS). Results: cfDNA levels in plasma and serum were significantly higher in patients with severe multiple trauma (SMT) than in those with moderate trauma (p = 0.002, p = 0.003, respectively) or with single fractures (each p < 0.001). CfDNA in plasma and serum correlated very strongly with each other (R = 0.91; p < 0.001). The AUC in ROC curves for identification of SMT patients was 0.76 and 0.74 for cfDNA in plasma and serum, respectively—this was further increased to 0.84 by the combination of cfDNA and hemoglobin. Within the group of multiple trauma patients, cfDNA levels were significantly higher in more severely injured patients and patients with severe traumatic brain injury (GCS ≤ 8 versus GCS > 8). Thirteen (20.3%) of the multiple trauma patients died during the first week after trauma. Levels of cfDNA were significantly higher in non-surviving patients than in survivors (p < 0.001), reaching an AUC of 0.81 for cfDNA in both, plasma and serum, which was further increased by the combination with hemoglobin and leukocytes. Conclusions: cfDNA is valuable for estimation of trauma severity and prognosis of trauma patients.
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24
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Extracellular Vesicles as Biomarkers in Head and Neck Squamous Cell Carcinoma: From Diagnosis to Disease-Free Survival. Cancers (Basel) 2023; 15:cancers15061826. [PMID: 36980712 PMCID: PMC10046514 DOI: 10.3390/cancers15061826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) arising from different anatomical sites present with different incidences and characteristics, which requires a personalized treatment strategy. Despite the extensive research that has conducted on this malignancy, HNSCC still has a poor overall survival rate. Many attempts have been made to improve the outcomes, but one of the bottlenecks is thought to be the lack of an effective biomarker with high sensitivity and specificity. Extracellular vesicles (EVs) are secreted by various cells and participate in a great number of intercellular communications. Based on liquid biopsy, EV detection in several biofluids, such as blood, saliva, and urine, has been applied to identify the existence and progression of a variety of cancers. In HNSCC, tumor-derived EVs exhibit many functionalities by transporting diverse cargoes, which highlights their importance in tumor screening, the determination of multidisciplinary therapy, prediction of prognosis, and evaluation of therapeutic effects. This review illustrates the classification and formation of EV subtypes, the cargoes conveyed by these vesicles, and their respective functions in HNSCC cancer biology, and discloses their potential as biomarkers during the whole process of tumor diagnosis, treatment, and follow-up.
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25
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Martínez de Toda I, González-Sánchez M, Díaz-Del Cerro E, Valera G, Carracedo J, Guerra-Pérez N. Sex differences in markers of oxidation and inflammation. Implications for ageing. Mech Ageing Dev 2023; 211:111797. [PMID: 36868323 DOI: 10.1016/j.mad.2023.111797] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Sexual dimorphism is a key factor to consider in the ageing process given the impact that it has on life expectancy. The oxidative-inflammatory theory of ageing states that the ageing process is the result of the establishment of oxidative stress which, due to the interplay of the immune system, translates into inflammatory stress, and that both processes are responsible for the damage and loss of function of an organism. We show that there are relevant gender differences in a number of oxidative and inflammatory markers and propose that they may account for the differential lifespan between sexes, given that males display, in general, higher oxidation and basal inflammation. In addition, we explain the significant role of circulating cell-free DNA as a marker of oxidative damage and an inductor of inflammation, connecting both processes and having the potential to become a useful ageing marker. Finally, we discuss how oxidative and inflammatory changes take place differentially with ageing in each sex, which could also have an impact on the sex-differential lifespan. Further research including sex as an essential variable is needed to understand the grounds of sex differences in ageing and to better comprehend ageing itself.
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Affiliation(s)
- Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Mónica González-Sánchez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Estefanía Díaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Gemma Valera
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Julia Carracedo
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Natalia Guerra-Pérez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
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26
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Lower Circulating Cell-Free Mitochondrial DNA Is Associated with Heart Failure in Type 2 Diabetes Mellitus Patients. CARDIOGENETICS 2023. [DOI: 10.3390/cardiogenetics13010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Cell-free nuclear (cf-nDNA) and mitochondrial (cf-mDNA) DNA are released from damaged cells in type 2 diabetes mellitus (T2DM) patients, contributing to adverse cardiac remodeling, vascular dysfunction, and inflammation. The purpose of this study was to correlate the presence and type of cf-DNAs with HF in T2DM patients. A total of 612 T2DM patients were prescreened by using a local database, and 240 patients (120 non-HF and 120 HF individuals) were ultimately selected. The collection of medical information, including both echocardiography and Doppler imagery, as well as the assessment of biochemistry parameters and the circulating biomarkers, were performed at baseline. The N-terminal brain natriuretic pro-peptide (NT-proBNP) and cf-nDNA/cf-mtDNA levels were measured via an ELISA kit and real-time quantitative PCR tests, respectively. We found that HF patients possessed significantly higher levels of cf-nDNA (9.9 ± 2.5 μmol/L vs. 5.4 ± 2.7 μmol/L; p = 0.04) and lower cf-mtDNA (15.7 ± 3.3 μmol/L vs. 30.4 ± 4.8 μmol/L; p = 0.001) than those without HF. The multivariate log regression showed that the discriminative potency of cf-nDNA >7.6 μmol/L (OR = 1.07; 95% CI = 1.03–1.12; p = 0.01) was higher that the NT-proBNP (odds ratio [OR] = 1.10; 95% confidence interval [CI] = 1.04–1.19; p = 0.001) for HF. In conclusion, we independently established that elevated levels of cf-nDNA, originating from NT-proBNP, were associated with HF in T2DM patients.
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Buzova D, Braghini MR, Bianco SD, Lo Re O, Raffaele M, Frohlich J, Kisheva A, Crudele A, Mosca A, Sartorelli MR, Balsano C, Cerveny J, Mazza T, Alisi A, Vinciguerra M. Profiling of cell-free DNA methylation and histone signatures in pediatric NAFLD: A pilot study. Hepatol Commun 2022; 6:3311-3323. [PMID: 36264206 PMCID: PMC9701487 DOI: 10.1002/hep4.2082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/19/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy-proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin-like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O-acyltransferase domain containing 7 (MBOAT7), and klotho-β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell-free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high-density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and function.
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Affiliation(s)
- Diana Buzova
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Maria Rita Braghini
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Salvatore Daniele Bianco
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Oriana Lo Re
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria
| | - Marco Raffaele
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Jan Frohlich
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Antoniya Kisheva
- Department of Internal Diseases IMedical University of VarnaVarnaBulgaria
| | - Annalisa Crudele
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Antonella Mosca
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Maria Rita Sartorelli
- Hepatology, Gastroenterology and Nutrition UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Clara Balsano
- Department of LifeHealth & Environmental Sciences‐ MESVA‐School of Emergency and Urgency Medicine, University of L'AquilaL'AquilaItaly
| | - Jan Cerveny
- Department of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Tommaso Mazza
- Laboratory of BioinformaticsFondazione IRCCS Casa Sollievo della SofferenzaSan Giovanni Rotondo (FG)Italy
| | - Anna Alisi
- Unit of Molecular Genetics of Complex PhenotypesBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Manlio Vinciguerra
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic,Department of Translational Stem Cell BiologyResearch Institute of the Medical University of VarnaVarnaBulgaria,Liverpool Center for Cardiovascular ScienceLiverpool Johns Moore UniversityLiverpoolUK
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28
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Advances in Endothelial Cell Biology: From Knowledge to Control. Int J Mol Sci 2022; 23:ijms23126403. [PMID: 35742847 PMCID: PMC9224320 DOI: 10.3390/ijms23126403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
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29
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Ershova ES, Shmarina GV, Porokhovnik LN, Zakharova NV, Kostyuk GP, Umriukhin PE, Kutsev SI, Sergeeva VA, Veiko NN, Kostyuk SV. In Vitro Analysis of Biological Activity of Circulating Cell-Free DNA Isolated from Blood Plasma of Schizophrenic Patients and Healthy Controls. Genes (Basel) 2022; 13:genes13030551. [PMID: 35328103 PMCID: PMC8955124 DOI: 10.3390/genes13030551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia is associated with low-grade systemic inflammation. Circulating cell-free DNA (c-cfDNA) belongs to the DAMP class. The major research question was: can the c-cfDNA of schizophrenic patients (sz-cfDNA) stimulate the DNA sensor genes, which control the innate immunity? We investigated the in vitro response of ten human skin fibroblast (HSF) lines to five DNA probes containing different amounts of a GC-rich marker (the ribosomal repeat) and a DNA oxidation marker (8-oxodG) including sz-cfDNA and healthy control c-cfDNA (hc-cfDNA) probes. After 1 h, 3 h, and 24 h of incubation, the expression of 6 protein genes responsible for cfDNA transport into the cell (EEA1 and HMGB1) and the recognition of cytosolic DNA (TLR9, AIM2, STING and RIG-I) was analyzed at the transcriptional (RT-qPCR) and protein level (flow cytometry and fluorescence microscopy). Additionally, we analyzed changes in the RNA amount of 32 genes (RT-qPCR), which had been previously associated with different cellular responses to cell-free DNA with different characteristics. Adding sz-cfDNA and hc-cfDNA to the HSF medium in equal amounts (50 ng/mL) blocked endocytosis and stimulated TLR9 and STING gene expression while blocking RIG-I and AIM2 expression. Sz-cfDNA and hc-cfDNA, compared to gDNA, demonstrated much stronger stimulated transcription of genes that control cell proliferation, cytokine synthesis, apoptosis, autophagy, and mitochondrial biogenesis. No significant difference was observed in the response of the cells to sz-cfDNA and hc-cfDNA. Sz-cfDNA and hc-cfDNA showed similarly high biological activity towards HSFs, stimulating the gene activity of TLR9 and STING DNA sensor proteins and blocking the activity of the AIM2 protein gene. Since the sz-cfDNA content in the patients’ blood is several times higher than the hc-cfDNA content, sz-cfDNA may upregulate pro-inflammatory cytokines in schizophrenia.
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Affiliation(s)
- Elizaveta S. Ershova
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Galina V. Shmarina
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Lev N. Porokhovnik
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Correspondence:
| | - Natalia V. Zakharova
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - George P. Kostyuk
- N.A. Alekseev Clinical Psychiatric Hospital No. 1, 117152 Moscow, Russia; (N.V.Z.); (G.P.K.)
| | - Pavel E. Umriukhin
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
- Department of Physiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey I. Kutsev
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Vasilina A. Sergeeva
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Natalia N. Veiko
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
| | - Svetlana V. Kostyuk
- Molecular Biology Laboratory, Research Centre for Medical Genetics, 115522 Moscow, Russia; (E.S.E.); (G.V.S.); (P.E.U.); (S.I.K.); (V.A.S.); (N.N.V.); (S.V.K.)
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Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022; 28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
Abstract
Collection and analysis of circulating tumor DNA (ctDNA) is one of the few methods of liquid biopsy that measures generalizable and tumor specific molecules, and is one of the most promising approaches in assessing the effectiveness of cancer care. Clinical assays that utilize ctDNA are commercially available for the identification of actionable mutations prior to treatment and to assess minimal residual disease after treatment. There is currently no clinical ctDNA assay specifically intended to monitor disease response during treatment, partially due to the complex challenge of understanding the biological sources of ctDNA and the underlying principles that govern its release. Although studies have shown pre- and post-treatment ctDNA levels can be prognostic, there is evidence that early, on-treatment changes in ctDNA levels are more accurate in predicting response. Yet, these results also vary widely among cohorts, cancer type, and treatment, likely due to the driving biology of tumor cell proliferation, cell death, and ctDNA clearance kinetics. To realize the full potential of ctDNA monitoring in cancer care, we may need to reorient our thinking toward the fundamental biological underpinnings of ctDNA release and dissemination from merely seeking convenient clinical correlates.
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Affiliation(s)
- Christopher T. Boniface
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
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